Most humans infected with H. pylori (Hp) are asymptomatic and do not develop severe pathology. Hp may benefit us by protecting against GERD and esophageal Ca. Thus, the challenge is to identify Hp+ individuals who are at greatest risk for developing severe disease and reserve treatment for them. A subset of Hp-infected hosts develops chronic atrophic gastritis (ChAG), characterized in part by loss of acid-producing parietal cells (PCs). The annual incidence of gastric adenocarcinoma (Ca) in patients with ChAG is 0.1-0.8%. During the last grant cycle, we used a gnotobiotic transgenic mouse model (tox176) with an engineered ablation of PCs to show that PC loss provides an opportunity for Hp to bind to, enter, and persist within gastric stem cells. We now propose 3 aims designed to examine how ChAG and this potentially dangerous 'liaison'influence Hp genome evolution and gastric epithelial progenitor (GEP) biology: (1) Define Hp genome evolution as individual human hosts progress to ChAG and to cancer. We will use the massively parallel GS-20 pyrosequencer to obtain deep draft whole genome sequences of 100 Hp isolates obtained from serial endoscopies of 5 patients enrolled in a completed study of 2 Swedish communities: 2 patients progressed from a normal gastric mucosa to ChAG during the 4 year interval between their endoscopic examinations;1 progressed from ChAG to Ca;2 maintained a normal mucosa. Our computational analysis will focus on identifying genes undergoing positive selection during the normal-ChAG and ChAG-Ca transitions. (2) Further correlate Hp evolution with host pathology using isolates from a case-control study of gastric Ca. To identify changes most likely to be biological relevant, we will prioritize the list using the analysis from aim 1 plus 3 criteria: (i) strength of positive selection in strains from the 5 index patients;(ii) significance of their difference in frequency between ChAG and Ca isolates;(iii) functional clustering (membership in metabolic/signaling pathways). Prioritized genes/mutations will be examined using multi-locus sequence typing in other isolates from the 5 index patients, plus 52 strains from 52 patients with normal gastric histology, ChAG or Ca enrolled in a separate, completed Swedish case-control study of gastric Ca. (3) Define the impact of Hp genome evolution on GEP biology. Interactions between 3 sequenced isolates with archetypal normal-, ChAG- and Ca-associated genotypes (defined from aims 1+2) and a model (m)GEP cell line we isolated from transgenic mice will be characterized using functional genomic (GeneChip, qRT-PCR) and transcriptome-directed biochemical analyses. Follow-up studies will involve colonization of gnotobiotic tox176 and normal mice with these strains and assaying for selected responses observed in mGEP cells. Results from these model systems will be applied to gastric biopsies obtained from the 5 index patients and case-control study. These analyses should provide the first genome-wide view of Hp evolution in ChAG and Ca, and yield new bacterial and host biomarkers associated with these states.